Job ID = 6459106 SRX = SRX6386777 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:11:04 prefetch.2.10.7: 1) Downloading 'SRR9624509'... 2020-06-21T13:11:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:20:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:20:03 prefetch.2.10.7: 1) 'SRR9624509' was downloaded successfully Read 53730154 spots for SRR9624509/SRR9624509.sra Written 53730154 spots for SRR9624509/SRR9624509.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:05 53730154 reads; of these: 53730154 (100.00%) were unpaired; of these: 19751637 (36.76%) aligned 0 times 24302043 (45.23%) aligned exactly 1 time 9676474 (18.01%) aligned >1 times 63.24% overall alignment rate Time searching: 00:12:05 Overall time: 00:12:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 19842805 / 33978517 = 0.5840 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 22:41:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:41:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:47: 1000000 INFO @ Sun, 21 Jun 2020 22:41:53: 2000000 INFO @ Sun, 21 Jun 2020 22:41:58: 3000000 INFO @ Sun, 21 Jun 2020 22:42:04: 4000000 INFO @ Sun, 21 Jun 2020 22:42:09: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 22:42:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:42:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:42:15: 6000000 INFO @ Sun, 21 Jun 2020 22:42:18: 1000000 INFO @ Sun, 21 Jun 2020 22:42:21: 7000000 INFO @ Sun, 21 Jun 2020 22:42:25: 2000000 INFO @ Sun, 21 Jun 2020 22:42:28: 8000000 INFO @ Sun, 21 Jun 2020 22:42:31: 3000000 INFO @ Sun, 21 Jun 2020 22:42:34: 9000000 INFO @ Sun, 21 Jun 2020 22:42:37: 4000000 INFO @ Sun, 21 Jun 2020 22:42:40: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 22:42:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:42:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:42:43: 5000000 INFO @ Sun, 21 Jun 2020 22:42:47: 11000000 INFO @ Sun, 21 Jun 2020 22:42:48: 1000000 INFO @ Sun, 21 Jun 2020 22:42:50: 6000000 INFO @ Sun, 21 Jun 2020 22:42:53: 12000000 INFO @ Sun, 21 Jun 2020 22:42:55: 2000000 INFO @ Sun, 21 Jun 2020 22:42:56: 7000000 INFO @ Sun, 21 Jun 2020 22:42:59: 13000000 INFO @ Sun, 21 Jun 2020 22:43:01: 3000000 INFO @ Sun, 21 Jun 2020 22:43:02: 8000000 INFO @ Sun, 21 Jun 2020 22:43:06: 14000000 INFO @ Sun, 21 Jun 2020 22:43:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:43:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:43:07: #1 total tags in treatment: 14135712 INFO @ Sun, 21 Jun 2020 22:43:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:43:07: #1 tags after filtering in treatment: 14135712 INFO @ Sun, 21 Jun 2020 22:43:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:07: 4000000 INFO @ Sun, 21 Jun 2020 22:43:08: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 22:43:08: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:08: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:08: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:08: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:08: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 22:43:08: #2 alternative fragment length(s) may be 2,40,597 bps INFO @ Sun, 21 Jun 2020 22:43:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.05_model.r WARNING @ Sun, 21 Jun 2020 22:43:08: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:43:08: #2 You may need to consider one of the other alternative d(s): 2,40,597 WARNING @ Sun, 21 Jun 2020 22:43:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:43:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:09: 9000000 INFO @ Sun, 21 Jun 2020 22:43:13: 5000000 INFO @ Sun, 21 Jun 2020 22:43:15: 10000000 INFO @ Sun, 21 Jun 2020 22:43:20: 6000000 INFO @ Sun, 21 Jun 2020 22:43:21: 11000000 INFO @ Sun, 21 Jun 2020 22:43:26: 7000000 INFO @ Sun, 21 Jun 2020 22:43:28: 12000000 INFO @ Sun, 21 Jun 2020 22:43:32: 8000000 INFO @ Sun, 21 Jun 2020 22:43:34: 13000000 INFO @ Sun, 21 Jun 2020 22:43:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:38: 9000000 INFO @ Sun, 21 Jun 2020 22:43:40: 14000000 INFO @ Sun, 21 Jun 2020 22:43:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:43:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:43:41: #1 total tags in treatment: 14135712 INFO @ Sun, 21 Jun 2020 22:43:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:43:41: #1 tags after filtering in treatment: 14135712 INFO @ Sun, 21 Jun 2020 22:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:43: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 22:43:43: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:43: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:43: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:43: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:43: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 22:43:43: #2 alternative fragment length(s) may be 2,40,597 bps INFO @ Sun, 21 Jun 2020 22:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.10_model.r WARNING @ Sun, 21 Jun 2020 22:43:43: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:43:43: #2 You may need to consider one of the other alternative d(s): 2,40,597 WARNING @ Sun, 21 Jun 2020 22:43:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:43:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:44: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:43:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.05_summits.bed INFO @ Sun, 21 Jun 2020 22:43:49: Done! pass1 - making usageList (892 chroms): 2 millis pass2 - checking and writing primary data (3830 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:50: 11000000 INFO @ Sun, 21 Jun 2020 22:43:56: 12000000 INFO @ Sun, 21 Jun 2020 22:44:01: 13000000 INFO @ Sun, 21 Jun 2020 22:44:07: 14000000 INFO @ Sun, 21 Jun 2020 22:44:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:44:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:44:08: #1 total tags in treatment: 14135712 INFO @ Sun, 21 Jun 2020 22:44:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:44:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:44:08: #1 tags after filtering in treatment: 14135712 INFO @ Sun, 21 Jun 2020 22:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:44:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:44:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:44:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:09: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 22:44:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:44:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:44:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:44:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:44:09: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 22:44:09: #2 alternative fragment length(s) may be 2,40,597 bps INFO @ Sun, 21 Jun 2020 22:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.20_model.r WARNING @ Sun, 21 Jun 2020 22:44:09: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:44:09: #2 You may need to consider one of the other alternative d(s): 2,40,597 WARNING @ Sun, 21 Jun 2020 22:44:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:44:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:44:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.10_summits.bed INFO @ Sun, 21 Jun 2020 22:44:22: Done! pass1 - making usageList (698 chroms): 2 millis pass2 - checking and writing primary data (2778 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:44:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386777/SRX6386777.20_summits.bed INFO @ Sun, 21 Jun 2020 22:44:50: Done! pass1 - making usageList (485 chroms): 2 millis pass2 - checking and writing primary data (1535 records, 4 fields): 14 millis CompletedMACS2peakCalling